Photoswitchable fluorescent probes are central to localization-based super-resolution microscopy. Among these probes, fluorescent proteins are appealing because they are genetically encoded. Moreover, the ability to achieve a one to one labeling ratio between the fluorescent protein and the protein of interest makes them attractive for quantitative single molecule counting. The percentage of fluorescent protein that is photoactivated into a fluorescently detectable form (i.e. photoactivation efficiency) plays a critical role in properly interpreting the quantitative information. It is important to characterize the photoactivation efficiency at the single molecule level to replicate the conditions used in super-resolution imaging. Here, we used the human Glycine receptor expressed in Xenopus oocytes and stepwise photobleaching or single molecule counting-PALM to determine the percentage of photoactivated fluorescent protein for mEos2, mEos3.1, mEos3.2, Dendra2, mClavGR2, mMaple, PA-GFP and PA-mCherry. This analysis provides important information that must be considered when using these fluorescent proteins in quantitative super-resolution microscopy.